Investigators have made "operator error" the focus of a probe into how a Boston Red Line train ended up leaving Braintree station Thursday morning without an MBTA driver at its helm.

The operator, a 51-year-old who had worked with the MBTA for more than 25 years, has been placed on paid leave while an investigation is underway, officials said.

About 50 passengers were on board the train as it traveled north before stopping past North Quincy station without a driver, Transportation Secretary Stephanie Pollack said in a news conference Thursday night.

Pollack called the incident an “unacceptable breach” of the T’s safety mandate. “We failed our passengers today,” she said.

The trouble began when the train stopped during a signal error at Braintree station, MBTA Chief Operating Officer Jeff Gonneville told reporters. The driver received approval to exit the train, then flipped a “bypass” switch, designed to allow the train to travel pass the signal, Gonneville said. But for reasons currently being investigated, the train began moving down the tracks, he said.

The driver sustained minor injuries when he was clipped by the train, MBTA spokesman Joe Pesaturo said. No passengers reported injuries, Pollack said.

Gonneville said train overseers knew in about 60 seconds that the driverless train had pulled away and began moving other trains further down the track out of the way. In fewer than 10 minutes, after the T cut power to the electrified third rail, the train came to a stop, Pollack said.

Investigators from several departments plan to regroup Friday morning, and officials said more information would be made available when it is complete. There was no discussion at the meeting of criminal charges.

The FBI and Massachusetts State Police have spoken with the T but determined they do not need to join the investigation, Pollack said. The National Transportation Safety Board has not made a decision on whether to participate, she said.

As of 2011, MBTA trains have only one operator, a policy that began to take effect in the 1990s, Gonneville said. Previously, each train had two.

Earlier Thursday, Gov. Charlie Baker said the investigation into the incident would include whether what happened on the train was “negligence versus something else.”

He also said it was “pretty clear” the controls in the train had been “tampered with,” though he felt the incident was “isolated.”

T officials Thursday night could not comment on the specific conditions of the controls on the train, which is being held at Cabot Yard in South Boston.

T General Manager Frank DePaola, also earlier in the day, called the incident "highly troubling."

"We had no idea what happened... When we arrived at JFK we overheard people saying that there was definitely no conductor. It was so unusual," she said, adding that rumors started flying that someone had been shot and that there was a power outage.

"The car just started going slow, the lights started flickering then all the lights went off. It stopped and we heard nothing. We knocked on the doors, people were trying to get out," she said.